The Scientist is linking to an imaginary1 article from PNAS in which researchers compare the cost of sequencing microbial (I’m guessing they mean bacteria) genomes using the traditional Sanger method and the hot new technology developed by 454. Not so surprisingly, they find that a hybrid method — ~5x coverage with Sanger followed by a couple rounds of 454 — is the most cost effective strategy. I say it’s not surprising because usually some intermediate solution wins out in science.
The Sanger method is nice because you get paired end reads from clones, which are very helpful in assembling shotgun sequenced genomes. If you thought shotgun sequencing was messy (compared to sequencing mapped clones), then strategies that take advantage of the 454 technology will make Pig-Pen look like Sean Connery to you. Researchers are currently using 454 to resequence bacterial genomes, and I think some work has been done using 454 for de novo genome sequencing in bacteria. The technology is currently not tractable for de novo sequencing of eukaryotic genomes, but this study suggest that 454 may prove useful in a clean-up role after some shotgun Sanger sequence has been generated.
1- They claim the article exists, and it just hasn’t been posted on the PNAS webpage yet.